# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:40:44 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)OCCN1[C@@H](CCN2C(=O)C=C(N=C12)N3CCOCC3)C(F)(F)F
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 RBQ  RBQ  (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one  ligand  52  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RBQ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 RBQ  C1    C  CR6   0   0.777   0.0369   0.7151   0.1357
 RBQ  N2    N  N     0  -0.546  -1.0576   0.2695   0.6749
 RBQ  N3    N  NR6   0  -0.573   0.0732   1.4843  -0.9771
 RBQ  C4    C  CR6   0   0.592  -2.2426   0.5964   0.1056
 RBQ  N5    N  NT    0  -0.527   1.2339   0.3475   0.6689
 RBQ  C6    C  CR6   0   0.564  -1.1166   1.9257  -1.5907
 RBQ  C7    C  CR16  0  -0.606  -2.3023   1.4479  -0.9902
 RBQ  C8    C  CH1   0  -0.293   2.3976   1.2053   0.6065
 RBQ  C9    C  CT    0   1.022   2.5480   1.9595   1.9255
 RBQ  N10   N  NT    0  -0.504  -3.3333   0.0731   0.7097
 RBQ  C11   C  CH2   0  -0.328   1.3670   1.7036  -1.6032
 RBQ  C12   C  CH2   0  -0.501   2.3308   2.2068  -0.5566
 RBQ  O13   O  O     0  -0.525  -1.0455   2.6461  -2.5845
 RBQ  F14   F  F     0  -0.303   2.7164   1.1474   2.9761
 RBQ  F15   F  F     0  -0.306   3.6056   2.7795   1.8947
 RBQ  F16   F  F     0  -0.305   1.4663   2.7042   2.1887
 RBQ  O17   O  O2    0  -0.482  -5.0760  -2.1427   0.7084
 RBQ  C18   C  CH2   0  -0.337   1.3246  -0.9342   1.3589
 RBQ  C19   C  CH2   0  -0.342  -4.6818   0.1918   0.1914
 RBQ  C20   C  CH2   0  -0.346  -3.2482  -0.9372   1.7500
 RBQ  C21   C  CH2   0  -0.158   1.0794  -2.0973   0.4179
 RBQ  O22   O  O2    0  -0.486   2.0158  -2.0254  -0.6250
 RBQ  C23   C  CH2   0  -0.180  -3.7635  -2.2625   1.2144
 RBQ  C24   C  CH2   0  -0.176  -5.1581  -1.1652  -0.3052
 RBQ  C25   C  CH1   0   0.052   1.6793  -2.7578  -1.7894
 RBQ  C26   C  CH3   0  -0.682   2.6407  -2.3286  -2.8816
 RBQ  C27   C  CH3   0  -0.685   1.7304  -4.2616  -1.5583
 RBQ  H111  H  HCH2  0   0.271   1.7160   0.7669  -2.0461
 RBQ  H112  H  HCH2  0   0.288   1.2455   2.4312  -2.3982
 RBQ  H7    H  HCR6  0   0.260  -3.2309   1.7458  -1.4502
 RBQ  H8    H  HCH1  0   0.316   3.2785   0.5702   0.4847
 RBQ  H181  H  HCH2  0   0.264   2.3281  -1.0190   1.7720
 RBQ  H182  H  HCH2  0   0.264   0.6295  -0.9862   2.1975
 RBQ  H121  H  HCH2  0   0.273   1.9929   3.1915  -0.2310
 RBQ  H122  H  HCH2  0   0.289   3.3228   2.3332  -0.9867
 RBQ  H191  H  HCH2  0   0.255  -5.3355   0.5444   0.9952
 RBQ  H192  H  HCH2  0   0.274  -4.7438   0.9192  -0.6127
 RBQ  H201  H  HCH2  0   0.283  -2.2224  -1.0408   2.0903
 RBQ  H202  H  HCH2  0   0.246  -3.8565  -0.6156   2.6017
 RBQ  H231  H  HCH2  0   0.243  -3.7888  -3.0055   2.0126
 RBQ  H232  H  HCH2  0   0.204  -3.0801  -2.6263   0.4332
 RBQ  H241  H  HCH2  0   0.208  -4.5596  -1.4603  -1.1790
 RBQ  H242  H  HCH2  0   0.244  -6.2019  -1.1046  -0.6167
 RBQ  H211  H  HCH2  0   0.221   1.1678  -3.0264   0.9965
 RBQ  H212  H  HCH2  0   0.207   0.0528  -2.0630   0.0302
 RBQ  H25   H  HCH1  0   0.196   0.6568  -2.4896  -2.0977
 RBQ  H261  H  HCH3  0   0.224   3.6680  -2.6032  -2.6345
 RBQ  H262  H  HCH3  0   0.228   2.3809  -2.8145  -3.8221
 RBQ  H263  H  HCH3  0   0.238   2.6031  -1.2503  -3.0421
 RBQ  H271  H  HCH3  0   0.236   1.0209  -4.5833  -0.7947
 RBQ  H272  H  HCH3  0   0.232   1.4810  -4.7921  -2.4779
 RBQ  H273  H  HCH3  0   0.223   2.7299  -4.5739  -1.2488

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 RBQ  C1   N2    double  1.299  0.020  1.299
 RBQ  C1   N3    single  1.353  0.020  1.353
 RBQ  C1   N5    single  1.361  0.020  1.361
 RBQ  N2   C4    single  1.355  0.020  1.355
 RBQ  N3   C6    single  1.410  0.020  1.410
 RBQ  N3   C11   single  1.454  0.020  1.454
 RBQ  C4   C7    double  1.389  0.020  1.389
 RBQ  C4   N10   single  1.352  0.020  1.352
 RBQ  N5   C8    single  1.447  0.020  1.447
 RBQ  N5   C18   single  1.458  0.020  1.458
 RBQ  C6   C7    single  1.412  0.020  1.412
 RBQ  C6   O13   double  1.230  0.020  1.230
 RBQ  C8   C9    single  1.527  0.020  1.527
 RBQ  C8   C12   single  1.536  0.020  1.536
 RBQ  C9   F14   single  1.338  0.020  1.338
 RBQ  C9   F15   single  1.339  0.020  1.339
 RBQ  C9   F16   single  1.339  0.020  1.339
 RBQ  N10  C19   single  1.450  0.020  1.450
 RBQ  N10  C20   single  1.453  0.020  1.453
 RBQ  C11  C12   single  1.509  0.020  1.509
 RBQ  O17  C23   single  1.412  0.020  1.412
 RBQ  O17  C24   single  1.411  0.020  1.411
 RBQ  C18  C21   single  1.516  0.020  1.516
 RBQ  C19  C24   single  1.521  0.020  1.521
 RBQ  C20  C23   single  1.520  0.020  1.520
 RBQ  C21  O22   single  1.403  0.020  1.403
 RBQ  O22  C25   single  1.416  0.020  1.416
 RBQ  C25  C26   single  1.517  0.020  1.517
 RBQ  C25  C27   single  1.522  0.020  1.522
 RBQ  C11  H111  single  0.970  0.020  1.090
 RBQ  C11  H112  single  0.970  0.020  1.090
 RBQ  C7   H7    single  0.930  0.020  1.080
 RBQ  C8   H8    single  0.970  0.020  1.090
 RBQ  C18  H181  single  0.970  0.020  1.090
 RBQ  C18  H182  single  0.970  0.020  1.090
 RBQ  C12  H121  single  0.970  0.020  1.090
 RBQ  C12  H122  single  0.970  0.020  1.090
 RBQ  C19  H191  single  0.970  0.020  1.090
 RBQ  C19  H192  single  0.970  0.020  1.090
 RBQ  C20  H201  single  0.970  0.020  1.090
 RBQ  C20  H202  single  0.970  0.020  1.090
 RBQ  C23  H231  single  0.970  0.020  1.090
 RBQ  C23  H232  single  0.970  0.020  1.090
 RBQ  C24  H241  single  0.970  0.020  1.090
 RBQ  C24  H242  single  0.970  0.020  1.090
 RBQ  C21  H211  single  0.970  0.020  1.090
 RBQ  C21  H212  single  0.970  0.020  1.090
 RBQ  C25  H25   single  0.970  0.020  1.090
 RBQ  C26  H261  single  0.970  0.020  1.090
 RBQ  C26  H262  single  0.970  0.020  1.090
 RBQ  C26  H263  single  0.970  0.020  1.090
 RBQ  C27  H271  single  0.970  0.020  1.090
 RBQ  C27  H272  single  0.970  0.020  1.090
 RBQ  C27  H273  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 RBQ  N5    C1   N3    116.88  3.000
 RBQ  N5    C1   N2    119.07  3.000
 RBQ  N3    C1   N2    123.98  3.000
 RBQ  C4    N2   C1    118.68  3.000
 RBQ  C11   N3   C6    121.10  3.000
 RBQ  C11   N3   C1    117.62  3.000
 RBQ  C6    N3   C1    120.88  3.000
 RBQ  N10   C4   C7    123.71  3.000
 RBQ  N10   C4   N2    115.11  3.000
 RBQ  C7    C4   N2    121.14  3.000
 RBQ  C18   N5   C8    119.43  3.000
 RBQ  C18   N5   C1    118.52  3.000
 RBQ  C8    N5   C1    122.03  3.000
 RBQ  O13   C6   C7    126.19  3.000
 RBQ  O13   C6   N3    119.11  3.000
 RBQ  C7    C6   N3    114.68  3.000
 RBQ  H7    C7   C6    116.62  3.000
 RBQ  H7    C7   C4    122.89  3.000
 RBQ  C6    C7   C4    120.44  3.000
 RBQ  H8    C8   C12   109.25  3.000
 RBQ  H8    C8   C9    107.69  3.000
 RBQ  C12   C8   C9    109.65  3.000
 RBQ  H8    C8   N5    107.97  3.000
 RBQ  C12   C8   N5    112.59  3.000
 RBQ  C9    C8   N5    109.56  3.000
 RBQ  F16   C9   F15   107.58  3.000
 RBQ  F16   C9   F14   106.54  3.000
 RBQ  F15   C9   F14   106.88  3.000
 RBQ  F16   C9   C8    111.40  3.000
 RBQ  F15   C9   C8    111.13  3.000
 RBQ  F14   C9   C8    113.00  3.000
 RBQ  C20   N10  C19   111.56  3.000
 RBQ  C20   N10  C4    122.81  3.000
 RBQ  C19   N10  C4    123.99  3.000
 RBQ  H112  C11  H111  108.27  3.000
 RBQ  H112  C11  C12   110.86  3.000
 RBQ  H111  C11  C12   111.27  3.000
 RBQ  H112  C11  N3    108.49  3.000
 RBQ  H111  C11  N3    109.23  3.000
 RBQ  C12   C11  N3    108.66  3.000
 RBQ  H122  C12  H121  107.18  3.000
 RBQ  H122  C12  C11   110.28  3.000
 RBQ  H121  C12  C11   108.07  3.000
 RBQ  H122  C12  C8    109.59  3.000
 RBQ  H121  C12  C8    112.09  3.000
 RBQ  C11   C12  C8    109.59  3.000
 RBQ  C24   O17  C23   111.75  3.000
 RBQ  H182  C18  H181  106.98  3.000
 RBQ  H182  C18  C21   109.73  3.000
 RBQ  H181  C18  C21   108.95  3.000
 RBQ  H182  C18  N5    111.48  3.000
 RBQ  H181  C18  N5    107.78  3.000
 RBQ  C21   C18  N5    111.75  3.000
 RBQ  H192  C19  H191  107.09  3.000
 RBQ  H192  C19  C24   109.74  3.000
 RBQ  H191  C19  C24   109.89  3.000
 RBQ  H192  C19  N10   111.88  3.000
 RBQ  H191  C19  N10   108.63  3.000
 RBQ  C24   C19  N10   109.57  3.000
 RBQ  H202  C20  H201  108.00  3.000
 RBQ  H202  C20  C23   109.99  3.000
 RBQ  H201  C20  C23   110.34  3.000
 RBQ  H202  C20  N10   108.68  3.000
 RBQ  H201  C20  N10   110.25  3.000
 RBQ  C23   C20  N10   109.53  3.000
 RBQ  H212  C21  H211  106.72  3.000
 RBQ  H212  C21  O22   111.09  3.000
 RBQ  H211  C21  O22   112.41  3.000
 RBQ  H212  C21  C18   110.26  3.000
 RBQ  H211  C21  C18   108.01  3.000
 RBQ  O22   C21  C18   108.30  3.000
 RBQ  C25   O22  C21   115.21  3.000
 RBQ  H232  C23  H231  107.99  3.000
 RBQ  H232  C23  C20   109.16  3.000
 RBQ  H231  C23  C20   110.12  3.000
 RBQ  H232  C23  O17   110.56  3.000
 RBQ  H231  C23  O17   107.37  3.000
 RBQ  C20   C23  O17   111.57  3.000
 RBQ  H242  C24  H241  107.98  3.000
 RBQ  H242  C24  C19   110.07  3.000
 RBQ  H241  C24  C19   109.17  3.000
 RBQ  H242  C24  O17   107.42  3.000
 RBQ  H241  C24  O17   110.69  3.000
 RBQ  C19   C24  O17   111.43  3.000
 RBQ  H25   C25  C27   108.32  3.000
 RBQ  H25   C25  C26   108.54  3.000
 RBQ  C27   C25  C26   111.56  3.000
 RBQ  H25   C25  O22   108.96  3.000
 RBQ  C27   C25  O22   112.21  3.000
 RBQ  C26   C25  O22   107.16  3.000
 RBQ  H263  C26  H262  107.79  3.000
 RBQ  H263  C26  H261  108.32  3.000
 RBQ  H262  C26  H261  107.90  3.000
 RBQ  H263  C26  C25   111.33  3.000
 RBQ  H262  C26  C25   110.13  3.000
 RBQ  H261  C26  C25   111.24  3.000
 RBQ  H273  C27  H272  108.01  3.000
 RBQ  H273  C27  H271  108.22  3.000
 RBQ  H272  C27  H271  107.34  3.000
 RBQ  H273  C27  C25   110.87  3.000
 RBQ  H272  C27  C25   110.17  3.000
 RBQ  H271  C27  C25   112.07  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 RBQ  CONST_01  C7    C4   N2   C1      0.00   0.0  0
 RBQ  CONST_02  N10   C4   N2   C1    180.00   0.0  0
 RBQ  CONST_03  C7    C6   N3   C1      0.00   0.0  0
 RBQ  CONST_04  C6    N3   C1   N2      0.00   0.0  0
 RBQ  CONST_05  C11   N3   C1   N2    180.00   0.0  0
 RBQ  CONST_07  C19   N10  C4   N2    180.00   0.0  0
 RBQ  CONST_08  C20   N10  C4   N2      0.00   0.0  0
 RBQ  CONST_09  C4    N2   C1   N3      0.00   0.0  0
 RBQ  CONST_11  N5    C1   N2   C4    180.00   0.0  0
 RBQ  CONST_12  C6    N3   C1   N5    180.00   0.0  0
 RBQ  CONST_13  C11   N3   C1   N5      0.00   0.0  0
 RBQ  CONST_14  C19   N10  C4   C7      0.00   0.0  0
 RBQ  CONST_15  C20   N10  C4   C7    180.00   0.0  0
 RBQ  CONST_16  C11   N3   C6   C7    180.00   0.0  0
 RBQ  CONST_17  O13   C6   N3   C1    180.00   0.0  0
 RBQ  CONST_20  O13   C6   N3   C11     0.00   0.0  0
 RBQ  Var_01    C12   C11  N3   C1    -52.42  30.0  1
 RBQ  Var_02    C8    C12  C11  N3     56.48  30.0  1
 RBQ  Var_03    C24   C19  N10  C4    109.80  30.0  1
 RBQ  Var_04    C23   C20  N10  C4   -110.12  30.0  1
 RBQ  Var_05    O17   C24  C19  N10    56.03  30.0  1
 RBQ  Var_06    O17   C23  C20  N10   -55.76  30.0  1
 RBQ  Var_07    C21   C18  N5   C1     64.21  30.0  3
 RBQ  Var_08    O22   C21  C18  N5     57.68  30.0  3
 RBQ  Var_09    C26   C25  O22  C21   168.35  30.0  3
 RBQ  Var_10    H261  C26  C25  O22    64.28  30.0  3
 RBQ  Var_11    H271  C27  C25  O22    61.41  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RBQ  chir_01  C8  N5  C9  C12  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 RBQ  plan-1  C1   0.020
 RBQ  plan-1  N2   0.020
 RBQ  plan-1  N3   0.020
 RBQ  plan-1  C4   0.020
 RBQ  plan-1  N5   0.020
 RBQ  plan-1  C6   0.020
 RBQ  plan-1  C7   0.020
 RBQ  plan-1  C8   0.020
 RBQ  plan-1  N10  0.020
 RBQ  plan-1  C11  0.020
 RBQ  plan-1  O13  0.020
 RBQ  plan-1  C18  0.020
 RBQ  plan-1  C19  0.020
 RBQ  plan-1  C20  0.020
 RBQ  plan-1  H7   0.020

